Penobscot River Restoration 2013 Newsletter

Volume 2, Issue 1 January 2013

PenobscotGreat Works Dam River Removal - A MilestoneResearch Event on the PenobscotNewsletter River The Great Works Dam removal marks Restoration Trust, some of the work was a pivotal time in the Penobscot River conducted by others. It is presented here Restoration Project. It represents a mile- as it describes the state of the ecosystem stone in a long process of engagement, and the collaborative science at this point work, and fundraising, and the beginning of in time. a new era of improved fish passage on the What the work suggests is that this Penobscot River. restoration enterprise has strong potential The occasion also marks the end of the for success and must be pursued with initial baseline science that has occurred sustained commitment. Dams impact fish. in the watershed for the last several years. This is well-known and it has been docu- During this period, researchers from Following dam removal, many of these mented here. Dams delay or prevent mi- academia, the Penobscot Indian Nation, studies are planned to resume so that a grations and they increase mortality. The non-profit groups, state and federal agen- clear before-after picture can be taken of stark contrast in alewife numbers between cies, and private consultants have been the effects of dam removal. The hope is Benton Falls (Kennebec River) and Veazie assessing the baseline condition of the that the lessons learned may be applied to (Penobscot) in 2011 — 3 million fish vs 2 Penobscot River watershed ecosystem. river, fish and ecosystem restoration efforts thousand fish — speaks volumes. Open They have collected data on fish passage, around the country and, possibly, around fish passage restores fish runs. Great geomorphology, water quality, wetlands, the world. Works is the pivotal first step towards the birds, mammals, and marine nutrients. The following articles are representa- Penobscot’s restoration. Congratulations! Although several studies will be ongoing tive of the scientific work that has been ~ Charlie Baeder, Monitoring Coordinator, during the next few years, others will be conducted in the Penobscot watershed the Penobscot River Restoration Trust on hold until after the lowermost dam, in last few years. Some of the work was con- Veazie, is also removed. ducted on behalf of the Penobscot River

Inside this issue: Acoustically Tagged Atlantic Salmon Smolt Survival in the

Great Works Dam Removal 1 Penobscot River and Estuary, 2010-2011

Salmon Smolt Survival 1 Joseph Zydlewski 1,2 Principal Investigator Daniel Stitch1, Ph.D. Student American Shad Restoration 2

1 Water Quality/Insect Monitoring 2 Department of Wildlife Ecology, University of Maine 2U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit Sea Lamprey Recolonization 3 Juvenile sea-run fishes require out) and give off a sonic code at a specific Geomorphic Process Model 4 uninterrupted passage through riverine frequency (69 kHz). The fish are then habitats in order to successfully reach the tracked on their seaward journey through Fish Community Assemblages 5 marine environment. During migration, the river using passive receivers. Since SONAR Monitoring 6 immediate or delayed mortality may 2005, an array of up to 178 stationary, result from predation, direct injury from acoustic receivers have been deployed Estuarine Fish Communities 7 turbines or other dam-related structures. and maintained in cooperation with Because impoundments differ in their NOAA National Marine Fisheries Service. PIT Tagging Adult Salmon 8 impact, quantifying passage success at These receivers have omni-directional specific sites is an important component of hydrophones, continuously monitoring at Acoustic Telemetry 9 programs that seek to maintain or restore 69 kHz. These receivers were deployed to Sedgeunkedunk Stream Monitoring 9 anadromous Atlantic salmon populations. cover the entire width of the river at each The purpose of this study was to site. When the receivers “hear” a tag, the Marine-derived Nutrients 10 characterize movement rates and survival tag identification, the date and time are of seaward migrating Atlantic salmon recorded. “You are What You Eat” 10 smolts in the Penobscot River. Tagging This sequence of detection allows the of the fish is accomplished by surgically estimation of survival using a Cormack- Shortnose Sturgeon 11 implanting an acoustic tag (about half the Jolly-Seber (CJS) mark-recapture model Geomorphic Monitoring 12 size of a triple A battery) and releasing and the calculation of movement rates the smolts upstream. The tags are active through specific river reaches, for example for several months (until their battery runs those with and without dams. cont. page 3 ... Mixing Technologies to Inform American Shad Restoration

Joseph Zydlewski 1,2 and Michael Bailey 1,3, Co-Principal Investigators Ann Grote1, M.S. Student

1Department of Wildlife Ecology, University of Maine Several years of 2U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit 3U.S. Fish and Wildlife Service

results indicate that The Penobscot River in Maine measuring the size of fish, and developing historically supported a tremendous size distributions in a system where abundance of migratory fishes including sampling methods are limited due to the in the Penobscot American shad. We have been working presence of threatened and endangered to understand the current status of this species. Analysis of the data indicates species and the scope for recovery after that in addition to Atlantic salmon and River, migrating the planned removal of two mainstem river herring, large numbers of American dams in 2012 and 2013 as part of the shad approach the dam but do not use Penobscot River Restoration Project. the fishway. Because Maine Department salmon move more Because the lowermost dam (Veazie of Marine Resources monitors the number Dam) is at the head of tide, spawning of Atlantic salmon successfully passing habitat for this species is limited, and the dam, these data provide a reference quickly through the very presence of this species was in for comparing viewed species-specific question. Removal of Veazie Dam and the encounters and ultimately an index of fish next up river dam (Great Works Dam) is abundance at the base of the dam. areas without dams anticipated to open up significant American More conventional approaches have shad habitat. We are using population also been use to assess habitat use and modeling to inform decision-making among behavior. In 2010 and 2011, American than those with potential proposed stocking scenarios. shad were captured via boat electrofishing The most significant uncertainty in the for telemetry work. This effort also provided recovery strategy has been the status an opportunity to collect age and spawning dams. Survival is of the current population. Beginning in data (via scales) as well as length data. 2009, Ann Grote began to blend old and Radio telemetry was used in the upper new technologies to inform managers river to characterize residence time and to markedly higher in of the current state of American shad in identify probable spawning areas. Acoustic the Penobscot River. The goals of this telemetry efforts exploited an extensive study are to address two main data gaps: acoustic array cooperatively deployed river reaches without characterization of adult shad migratory and maintained by the Maine CRU, the behavior and characterizing the existing University of Maine and NOAA Fisheries. river specific run. This array tracked adults leaving the dams. The work underway uses Dual- Penobscot River and entering the ocean, Frequency Identification Sonar (DIDSON). presumably after spawning. DIDSON works like an ultrasound camera, allowing researchers to “view” fish at Funded through The Nature Conservancy, night and in turbid water. By deploying NOAA-Fisheries, US Geological Survey a DIDSON camera at the base of Veazie Maine Cooperative Fish and Wildlife Dam, a continuous video record of fish Research Unit and the University of Maine approaching the base of the dam was recorded. This approach proved effective for making species determinations,

Benthic Macroinvertebrate and Water Quality Monitoring of Great Works and Veazie Dam Project Areas: Pre-dam Removal

Daniel H. Kusnierz1, Principal Investigator T. Jason Mitchell1,, Jan Paul1, Angela Reed1 and Rhonda Daigle1

1Penobscot Indian Nation, Water Resources Program

In 2009 and 2010, as part of the The primary objective of the monitoring Penobscot River Restoration Project is to determine if and how water quality (PRRP), the Penobscot Indian Nation and benthic invertebrate community Water Resources Program (PIN WRP) composition in the Lower Penobscot River conducted studies of water quality and changes with barrier removal. Additionally, benthic macroinvertebrates at select these data will have useful interpretive Rock-filled basket substrates used for sites in the lower Penobscot River. The value for other lower river research monitoring aquatic insects as water purpose of this monitoring was to gather projects. quality indicators. baseline data in advance of the removal of the Veazie and Great Works Dams, and continued on page 11 ... the construction of the Howland Bypass. Dam Removal In The Sedgeunkedunk Stream

Stephen M. Coghlan Jr. 1 and Joseph Zydlewski1,2, Co-Principal Investigators Kevin Simon3, Co-Investigator Robert S. Hogg1 and Corey Gardner 1,2, M.S. Students

1Department of Wildlife Ecology, University of Maine The increased return 2U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit 3 The University of Auckland, Auckland, NZ of sea lamprey Sedgeunkedunk Stream, a tributary to increase in the abundance of spawning sea the Penobscot River, historically supported lamprey, from less than 65 fish to more than several anadromous fish species including 250. may benefit other sea lamprey and Atlantic salmon. However, The increased return of sea lamprey two small dams constructed in the may benefit other species through their 1800s reduced or eliminated spawning spawning activity. Nest building of these species through runs entirely. In 2009, efforts to restore fish increases stream-bed complexity, marine-freshwater connectivity in the while reducing fine sediment accumulation system culminated with removal of the and proportion of embedded particles. their spawning lowermost dam making 5 km of stream These changes persist through summer habitat accessible to anadromous fish. Sea and into fall when Atlantic salmon lamprey utilized accessible habitat prior to spawners select these habitat qualities. activity. Nest dam removal and were chosen as a focal These changes may also benefit resident species to characterize recolonization. drift-feeding stream fishes including During sea lamprey spawning runs of juvenile Atlantic salmon. Thus the re- building of these fish 2008 through 2011 (pre- and post-dam colonization of Sedgeunkedunk Stream by removal), individuals were marked with sea lamprey may have lasting effects on passive integrated transponders (PIT stream community dynamics. increases stream- tags) and their activity was tracked by walking the stream daily and identifying Funded by Penobscot River Restoration the fish remotely. Population estimates Trust, NOAA-Fisheries, American bed complexity were derived using a modeling approach Recovery and Reinvestment Act, U.S. (POPAN extension of Program MARK). Geological Survey, Maine Cooperative After dam removal there was a four-fold Fish and Wildlife Research Unit. ... These changes persist through summer and into fall when Atlantic salmon spawners select these habitat qualities. Sea lamprey constructing a nest at Sedgeunkedunk Stream.

SALMON SMOLT SURVIVAL including Atlantic salmon, several of the ... cont. from page 1 dams that will remain in place greatly impact migrating juveniles. These results Several years of results indicate that in the underscore the importance of assessing Penobscot River, migrating salmon move both upstream and downstream migration. more quickly through areas without dams than those with dams. Survival is markedly Funded by Penobscot River Restoration higher in river reaches without dams. Trust, NOAA Fisheries, American Recovery Though these results are not unexpected, and Reinvestment Act, U.S. Geological some dams have more of an adverse Survey, Maine Cooperative Fish and effect on migration than others. While the Wildlife Research Unit, and Great Lakes removal of Great Works and Veazie Dams Hydro will greatly improve upstream access to spawning habitat for many species Developing and Testing a Geomorphic Process Model to Predict Median Bed Grain Size

Noah Snyder 1 Andy Nesheim 1, student The model performed 1 Boston College, Boston, MA best in alluvial Over the past several years, a team elevation models to measure channel of graduate and undergraduate geology parameters necessary as model inputs. students working with professor Noah He found that predicted bed grain size single-thread channel Snyder at Boston College have collected fell within a factor of two of the field-mea- geomorphic data from several rivers in sured median grain size in >70% of the Maine. A previous study (Wilkins & Snyder, study sites. The model performed best in segments with gravel- published in River Research and Applica- alluvial single-thread channel segments tions, 2011) involved mapping potential with gravel-cobble beds in the median Atlantic salmon habitat in the Narraguagus grain size range from 16 to 256 mm, which cobble beds in the River. Their most recent research focusing corresponds to ideal spawning and rearing on the West Branch of the Pleasant River habitat for Atlantic salmon. has a direct link to the ongoing restora- The model was less successful in median grain size range tion efforts on the Penobscot River (the depositional segments with relatively fine West Branch of the Pleasant River is a beds and greater channel variability. Model from 16 to 256 mm, tributary of the Piscataquis River, which failures occurred in segments that deviate enters the Penobscot River at Howland). from the single-thread gravel-bed channel This river is presently inaccessible to most type, and may indicate areas to focus res- which corresponds to anadromous species, but completion of toration efforts. These methods are useful the Penobscot River Restoration Project for detailed morphologic assessment, and should enable increased anadromous spe- this approach is an easily applied tool for ideal spawning and cies passage. predicting grain size and habitat suitability. This research formed the basis for An- Much of this research was just pub- drew Nesheim’s recent M.S. thesis, which lished in the January 2013 issue of rearing habitat for involved developing and testing a geo- Geological Society of America Bulletin. morphic process model to predict median Atlantic salmon. bed grain size. Andrew used standard and Funded by the National Science LiDAR (light detection and ranging) digital Foundation.

Figure 1. Median bed grain size predicted using a GIS-based model for a reach of the West Branch Pleasant River downstream from the Gulf Hagas canyon.

.. many diadromous fishes were restricted to tidal waters below Veazie Dam, although Atlantic salmon, sea lamprey,

Electrofishing the Penobscot River to survey fish assemblages pre-dam removal. and American eel Fish are stunned, held in a holding tank for identification and data collection, then released back to the river. Photos courtesy of Steve Coghlan. were captured or Quantifying the Structure of Fish Assemblages in the Penobscot River observed upstream. Stephen M. Coghlan Jr. 1, Principal Investigator Species richness Joseph Zydlewski1,2 and Daniel Hayes3, Co-Investigators Ian Kiraly1, M.S. Student was relatively high 1Department of Wildlife Ecology, University of Maine 2U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit below Veazie Dam ... 3Michigan State University Department of Fisheries and Wildlife These data indicate The Penobscot River once provided of the river was distinct in composition: spawning and juvenile rearing habitats many diadromous fishes were restricted to to migratory fish. The construction of tidal waters below Veazie Dam, although that the restoration dams blocked migrations of these fish Atlantic salmon, sea lamprey, and and fragmented habitats, changing the American eel were captured or observed structure of fish assemblages throughout upstream. Species richness was relatively of connectivity the river. The Penobscot River Restoration high below Veazie Dam. Lastly, areas Project is anticipated to increase passage above and below dams differed greatly of anadromous and resident fishes and in composition, with dam head ponds through dam removal improve the connectivity among currently favoring more warm water and lentic fragmented habitats. The purpose of this species. These data indicate that the study is to quantify and characterize fish restoration of connectivity through dam assemblages in the lower ~70 kilometers removal will likely result in predictable will likely result in of the Penobscot River, along with major shifts in fish assemblages. tributaries. This will aid in understanding the influence of fragmentation in a large Funded by Penobscot River Restoration predictable shifts in river system and provide a benchmark Trust, NOAA Restoration Center and the from which post-dam removal assessment American Recovery and Reinvestment can measure. Act, along with the USGS Maine fish assemblages.

Boat electrofishing surveys were Cooperative Fish and Wildlife Research conducted during 2010 and 2011, in both Unit, the University of Maine, and Maine the early summer and fall. “Stratified- Department of Inland Fish and Wildlife, random” sampling was conducted using The Nature Conservancy and the Maine 500 meter transects. Three factors Outdoor Heritage Trust had clear effects on fish assemblage composition. In general, fish assemblage structure differed according to longitudinal position along the river. The tidal section SONAR Sampling to Understand Changes in Penobscot River Fish Community Dynamics Resulting from Restoration Efforts

Gayle Zydlewski1, Principal Investigator Joseph Zydlewski2, Co-Investigator Patrick Erbland1, Ph.D. Student SONAR systems are 1School of Marine Sciences, University of Maine 2U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit used to monitor fish presence, abundance SONAR systems are used to monitor imaging, sampling and velocity profiling fish presence, abundance and movements that complement and confirm information in rivers, estuaries, and oceans. We have from the primary SONAR systems. and movements in been using this technology to monitor fish Data collected by other researchers passing through a cross section/ transect are also being used to verify/validate on the lower Penobscot River, near fish counts and identifications: boat rivers, estuaries, and Bangor/Brewer since 2010. Our goal is to electrofishing, acoustic and radio tag data measure and understand changes in fish of fish moving through the lower river, populations before and after the Penobscot fish collected in the Veazie fish trap, and oceans. We have been River Restoration Project. We have been mobile side-scan imaging surveys. Four- developing a standardized approach dimensional GIS software is being used to for long-term SONAR monitoring, and compile these datasets and provide a more using this technology collecting pre-restoration data that will be comprehensive picture of fish community the baseline for comparison in subsequent dynamics in the lower Penobscot. Future to monitor fish years following restoration activities. plans include annual deployment of these The SONAR systems are automated systems, enabling a long-term assessment to continually record fish passage of changes in fish presence as it is related passing through through a cross section of the river to pre- and post-dam removal conditions. from April to December (under ice-free This project is ongoing and funded by conditions) each year. In cooperation Penobscot River Restoration Trust through a cross section/ with the SONAR manufacturer and local the NOAA Restoration Center and the community members the systems have American Recovery and Reinvestment transect on the lower been optimized by: adjusting the SONAR Act and Open Rivers Initiative, and the to the river form; internet connections University of Maine. to field computers for real-time remote Penobscot River, near access; and implementing standardized Bangor/Brewer since 2010.

The Penobscot Estuarine Fish Community and Ecosystem Survey

Michael O’Malley1 J. Stevens1 Rory Saunders1 Christine Lipsky1 John Kocik 1 The multifrequency

1 NOAA Fisheries, Orono, ME split-beam method

In 2010, we began investigating novel target strength distributions varied across fish capture techniques and hydroacous- time and space during the survey period can provide fish and tics methods to monitor changes in species (May–June and Nov-Dec 2011). Dam composition over time and space in the removal upstream may cause changes in Penobscot estuary. The project began estuarine communities, and an expansion zooplankton biomass with an exploratory and descriptive phase of methods will be needed to investigate and is evolving into a study network where changes in fish and zooplankton popula- long-term monitoring, hypothesis testing, tions over larger spatio-temporal scales. data over larger scales and impact assessments will be possible. The multifrequency split-beam method Pelagic trawling, fyke netting and beach can provide fish and zooplankton biomass for relatively small seining in 2011 revealed multiple size data over larger scales for relatively small classes of alosines suggesting more exten- investment over the long term. Knowl- sive estuarine use than previously thought. edge gained from this study will improve investment over the We were excited that initial survey results our ability to: 1) manage estuaries in the also found contemporary evidence of natu- future and 2) conduct vital research on ral reproduction of American shad. the habitats and ecosystem services they long term. We conducted mobile transects using provide. The design specifics should be downward-looking SIMRAD EK60 split- transferable to multiple systems to develop beam (38 and 120 kHz) to provide acoustic a regional perspective. target strength and biomass distributions throughout the estuary. Using Sv Funded by NOAA National Marine dB differencing techniques to distinguish Fisheries Service, Northeast Fisheries fish and zooplankton, we found that fish Science Center and zooplankton biomass (NASC) and

Conducting downward looking mobile hydroacoustic transects using RV Silver Smolt on 07/01/2011. The two split-beam transducers (38 and 120 kHz) are held in place 0.5m below the surface from the port side with an aluminum frame.

Echograms of the water column from an area close to the Verona Bridges, 11/08/2011; individual fish distribution (top echogram) and zooplankton aggregations (bottom echogram).

Using PIT Telemetry to Track Adult Atlantic Salmon in the Penobscot River

Joseph Zydlewski 1,2 – Principal Investigator Douglas B. Sigourney 2 – Post-Doctoral Associate

Antennas (loops of 1U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit 2Department of Wildlife Ecology, University of Maine wire a tagged fish The Penobscot River is currently dams. In addition, live transport resulted impounded by five main stem dams in a significant decrease in transit time must swim through to impeding access to historic spawning from Veazie to the upstream dams. There grounds. In addition, there are also was also no apparent handling effect several dams on the major tributaries on passage: there was no difference in be “read”) are located to the Penobscot River including the success at the upstream dams among Passadumkeag and the Piscataquis rivers. adults that were transported and those near the entrances In cooperation with dam owners, we that were not. In 2012 and 2013, the two installed antennas at hydroelectric facilities lowest-most dams on the Penobscot River in the Penobscot River. Antennas (loops are scheduled for removal as part of the and exits of fishways of wire a tagged fish must swim through to Penobscot River Restoration Project. be “read”) are located near the entrances This research will provide pre-removal and exits of fishways. This arrangement assessment data to gauge the effects ... to determine if allows us to determine if a fish entered of dam removal. More importantly, this a fishway, and, if so, was it successful in effort is a collaborative enterprise that will passing upstream. Unlike past telemetry continue to inform management through a fish entered a studies that tracked the movements of the quantitative assessment of passage in a small number of fish, the use of PIT the Penobscot River. fishway, and, if so, tag technology allowed large numbers of fish to be tracked. These tags are small Funded by Penobscot River Restoration (about the size of 2 grains of rice), last Trust, NOAA-Fisheries, American was it successful in indefinitely, and are relatively inexpensive Recovery and Reinvestment Act, U.S. (less than $5.00/tag). Returning adults Geological Survey, Maine Cooperative are captured by the Maine Department of Fish and Wildlife Research Unit passing upstream Marine Resources at the lowest-most dam (Veazie Dam) and PIT-tagged before being released. ... the use of PIT tag PIT arrays and remote modem connections allow near real-time assessment of passage and management technology allowed actions. For example, results suggest that live transport resulted in a significant large numbers of fish increase in arrival success at the upstream to be tracked.

Atlantic salmon at the Veazie fish trap is checked for a PIT tag, measured and weighed before either being transported to the Craig Brook Fish Hatchery or released back into the river. Sedgeunkedunk Stream: One Piece of the Penobscot Puzzle

Stephen M. Coghlan Jr. 1, Joseph Zydlewski1,2 , Kevin Simon3, and Rory Saunders4, Principal Investigators

1Department of Wildlife Ecology, University of Maine 2U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit 3The University of Auckland, Auckland, NZ 4NOAA Fisheries, Orono, ME

Sedgeunkedunk Stream is a tributary of bution and abundance of resident and the Penobscot River that typifies small sea-run fishes in the watershed since streams in Maine impacted by low-head 2007. The removal of the lowermost dam dams. Runs of anadromous fishes in this resulted in striking changes in fish assem- system declined or disappeared after blage metrics and sea-run species gained Researchers are recording data on acous- the building of multiple dams within the access to up river habitat. Sedgeunkedunk tic telemetry receivers that are used to watershed. These declines mirror those Stream can serve as a model of what track Atlantic salmon smolt, hatchery and in the entire Penobscot watershed, which may result at a much larger scale through wild, on their migration to the ocean. contains over 100 known dams. As part the Penobscot River Restoration Project. of a collaborative restoration project, fish We view the Penobscot River structurally passage on Sedgeunkedunk Stream has and functionally as a network of several been restored by the removal of two dams hundred similarly-sized tributaries. The ef- between Fields Pond and the confluence fects of mainstem dam removal should be with the Penobscot River. The lowermost readily detectable and quantifiable in these dam (Mill Dam) was removed in August small watersheds. 2009, and the middle dam (Meadow Dam) was bypassed in August 2008 by a rock- Funded by NOAA-Fisheries, ramp fishway that allows fish passage U.S. Geological Survey, Maine while maintaining current water levels in Cooperative Fish and Wildlife Fields Pond and adjacent wetlands. Research Unit, Maine Sea Grant, and We have been monitoring the distri- The University of Maine

Acoustic Telemetry: An Established Monitoring Tool for Assessing Pre-dam Removal Conditions for Diadromous Fishes of the Penobscot River

James Hawkes1 , Graham Goulette1 ,,Joe Zydlewski3 , Gayle Zydlewski2 , and John Kocik1 , Principal Investigators

1 NOAA Fisheries, Orono, ME An acoustic tag surgically inserted into 2School of Marine Sciences, University of Maine a salmon smolt before release back 3U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit into the river.

Acoustic telemetry is a modern salmon and shortnose sturgeon that are able to identify any changes of habitat use, research tool that allows researchers to protected under the US Endangered Spe- behaviors and migration corridors as spe- remotely monitor tagged animals. Passive cies Act. Additionally, with the Penobscot cies are reintroduced to areas that have fixed position receiver networks collect River Restoration Project in early planning been inaccessible for decades. temporal data to provide information on phases, research on pre-restoration fish migration behavior, routes, areas of high ecology was particularly important. Funded by Penobscot River Restoration mortality as well as seasonal activity pat- As a result, data collected since 2005 Trust, NOAA, National Marine Fisheries terns of individual animals. The National have been used for risk assessment of Service, Northeast Fisheries Science Cen- Oceanic and Atmospheric Administration, proposed in-stream construction and repair ter, America’s Recovery and Reinvestment University of Maine and United States or removal activities which may threaten Act, U.S. Fish and Wildlife Service, USGS Geological Survey have deployed an fish during migration periods or sensitive Maine Cooperative Unit, Great Lakes extensive array of more than 100 telemetry periods during their life history. Addition- Hydro receivers in the Penobscot River, estu- ally, these data provide documentation of ary and Bay each year since 2005. This habitat use of fish prior to dam removal array has been used to monitor several and other proposed restoration activities. diadromous fish species, including Atlantic Once dam removal has occurred we will be

“You are What You Eat”: Using Stable Isotopes to Assess Freshwa- ter and Marine Food Web Change in Response to Dam Removal

Karen Wilson1 Graham Sherwood2

Barrier removal 1Dept of Environmental Science, University of Southern Maine 2Gulf of Maine Research Institute, Portland, ME in the Penobscot A primary objective of the Penobscot River idea that ‘you are what you eat’ because Restoration Project is to improve anad- isotope signatures of consumers reflect the River drainage romous fish passage between the upper isotope values of their prey, which in turn reaches of the river and the nearshore can be used to infer food chain level and marine environment. Increased connectiv- habitat associations (in this case marine is anticipated ity is expected to positively impact resi- vs. freshwater). Pre-dam removal data col- dent biota in both marine and freshwater lected in 2009-2011 shows strong isotopic environments in part by providing food distinctions between the freshwater and to improve web subsidies from the adjacent ecosys- marine food webs. We found intriguing in- tem. In the freshwater system, spawning termediate signatures in roving nearshore anadromous fishes (e.g., river herring) are marine predators such as mackerel who connectivity for expected to add marine-derived nutrients are known to eat out-migrating juvenile to lakes and rivers. In the marine system, river herring. This approach provides reli- Atlantic salmon and it is expected that juvenile anadromous able and cost effective indicators of food fishes out-migrating from freshwater nurs- web change in response to dam removals. ery habitat will be consumed by nearshore other anadromous marine predators (e.g., cod). In order Funded by The Nature Conservancy, to quantify linkages between these two and Penobscot River Restoration Trust, systems, we are using stable isotopes to through the NOAA Restoration Center and species within their estimate energy flows before (this study) the American Recovery and Reinvestment and after (future study) dam removals. Act. historic spawning Stable isotope studies are based on the

habitat. There is, Effects of Marine-derived Nutrients on Juvenile Atlantic Salmon and Their Communities however, a likely Cynthia Loftin1,2 and Joseph Zydlewski1,2, Co-Principal Investigators 1 second effect. The Margaret Guyette , Ph.D. Student 1Department of Wildlife Ecology, University of Maine resultant marine 2U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit

Prior to dam construction in the than in controls. nutrient pulses may Penobscot River watershed, Atlantic Barrier removal in the Penobscot salmon and other anadromous species River drainage is anticipated to improve transported marine-derived nutrients to connectivity for Atlantic salmon and other increase Atlantic freshwater systems during spawning anadromous species within their historic events in the form of metabolic expenditure spawning habitat. There is, however, a and through decomposition of mortalities. likely second effect. The resultant marine salmon success These contributions may have strongly nutrient pulses may increase Atlantic influenced productivity in otherwise salmon success in their early life stages nutrient limited systems, influencing many through direct and indirect uptake. in their early life components of the stream community. Such input may have bolstered the growth Funding through NOAA-Fisheries, US and survival of young Atlantic salmon. Geological Survey Maine Cooperative To test this hypothesis, we stocked stages through Fish and Wildlife Research Unit and the four headwater streams with young-of- University of Maine the-year Atlantic salmon and manipulated direct and indirect nutrient input with a carcass analog timed to match sea lamprey and Atlantic salmon spawning. We documented nutrient uptake uptake. by Atlantic salmon and macroinvertebrates using nitrogen and carbon “stable isotopes”. Interestingly, young-of-the- year Atlantic salmon were larger and had greater fat reserves in treatment reaches 10 continued from page 2 ... prior to dam removal we collected water samples and measurements from 10 sites We monitored aquatic benthic within the Great Works and Veazie dams macroinvertebrates from (7) locations project areas. Water quality parameters associated within the impoundment and collected included dissolved oxygen, tailwater areas of the Great Works and temperature, conductivity, BOD, bacteria, Veazie dams, as well as the tailwater turbidity, secchi transparency, total area of the Milford Dam. Following Maine suspended solids, pH, chlorophyll ā, and Shortnose sturgeon DEP methods, we deployed rock filled total phosphorous. Stations were sampled baskets as artificial substrates in triplicate late-July thru late-October, 2009 and mid- sets and allowed them to be colonized by June thru late-October, 2010 at 1-2 week have not been benthos for 28 ± days. The contents of intervals. Additionally we deployed Onset the substrates were removed, sorted, and Hobo temperature loggers at 15 locations sent to a taxonomist for identification and associated with the Great Works, Veazie, documented enumeration. These data will be used and Howland dam areas and at select free for assessing changes in the aquatic life flowing areas. These recorders collected community structure due to dam removal water temperature data continuously at spawning in the and for determining whether aquatic life 30 minute intervals. Pending funding criteria are attained. Attainment status we anticipate beginning post-removal and indices of community structure will be monitoring in 2013. analyzed using the Maine DEP aquatic life Penobscot River statistical model developed for rivers and Funding provided by Penobscot River streams in Maine. Restoration Trust through NOAA ARRA; To characterize water quality conditions BIA PL 638, EPA CWA Section 106. ...the presence of reproductive Shortnose Sturgeon of the Penobscot River

Gayle Zydlewski1, Principal Investigator females and suitable Michael Kinnison2, Co-Principal Investigator Joseph Zydlewski3, Co-Investigator spawning habitat in Matthew Altenritter, Ph.D. Student Matthew Wegener and Kevin Lachapelle, M.S. Students the upper river has 1School of Marine Sciences, University of Maine 2School of Biology and Ecology, University of Maine been documented. 3U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit Reproductive Until recently, the presence of endangered shortnose sturgeon use the Penobscot shortnose sturgeon in the Penobscot River River throughout the year. Shortnose was undocumented but presumed based sturgeon have not been documented females from on a single animal caught in Penobscot spawning in the Penobscot River, Bay in 1978. In 2006, their presence was although the presence of reproductive confirmed and research was initiated to females and suitable spawning habitat in the Penobscot document seasonal movement patterns, the upper river have been documented. use of the upper river, and to estimate the Reproductive females from the Penobscot size of the population. The primary method River have been documented moving to River have been used to document movement patterns is the Kennebec River, potentially indicating acoustic telemetry. Sturgeon are captured a complex reproductive migration documented moving using gill nets (under a research permit) pattern. Characterizing the movements, and carefully handled to implant a tag that population size, and reproductive patterns transmits a ping that can be recorded by of shortnose sturgeon in the Penobscot to the Kennebec special devices positioned throughout River provides a baseline for assessing the the river system. To estimate the size impact of the Penobscot River Restoration of the population, two methods, mark- Project and will elucidate the status of River, potentially recapture and acoustic imaging, have sturgeon populations throughout the Gulf been used. Mark-recapture estimates of Maine. have been made during summer and fall. indicating a complex During winter, shortnose sturgeon form This project is funded by the Maine dense aggregations. We can image these Department of Marine Resources through aggregations and count the number of fish reproductive an Endangered Species Act Section 6 present. Since only one annual wintering grant from NOAA-Fisheries; Penobscot site has been identified in the Penobscot, River Restoration Trust through the NOAA migration pattern. this gives us a population estimate of the Restoration Center and the American wintering shortnose sturgeon. Estimates to Recovery and Reinvestment Act, and the date are consistent between the methods and indicate that nearly 1,000 adult University of Maine. 11 Pre-Dam Removal Geomorphic Monitoring on the Penobscot River, Maine

Alice Kelley1 Daniel Belknap1 Andrew Heller1 Charles Baeder2 Matthias Collins3

1Department of Earth Sciences and Climate Change Institute, University of Maine 2Penobscot River Restoration Trust 3NOAA Restoration Center, Gloucester, MA

Dams change the geomorphic and repeated, seasonal photographic surveys, biologic characteristics of watersheds. bathymetric surveys at each cross section, Frequently, removal is seen as an effec- video-based channel sediment character- tive way to restore lost habitats and rebuild ization, bank geomorphology studies, and ecological communities. The largest of geophysical characterization of impound- these projects on the North American ment sediment thickness. Data collected East coast is currently being under taken have been uploaded to Google Earth, a in Maine. The Penobscot River Restora- freely available interactive satellite imagery tion Project plans to remove two dams display and mapping program, as a means and build a fish by-pass on the Penobscot of displaying information and providing River, in an effort to restore 11 species public access to spatially referenced data. of sea-run fish, while maintaining energy Over the two-year monitoring period, storage noted in many impoundments, production. The removal of the first dam is few changes were noted in river bathym- and is interpreted to be an artifact of the scheduled for summer of 2012. etry or bank characteristics. Channel region’s complex Late-Pleistocene and In anticipation of dam removal, geomor- sediment characterization revealed that, Holocene geological history. phic monitoring was undertaken at monu- within the study area, the Penobscot River mented river cross-sections within the dam channel in both flowing and impounded Funded by Penobscot River Restoration removal area to provide baseline data on reaches is dominated by coarse sediment Trust, through the NOAA Restoration channel bathymetry, sediment size, and with a predominately sand matrix. This is Center and the American Recovery and bank conditions. Data collection included in striking contrast to fine-grained sediment Reinvestment Act

The Penobscot River Restoration Trust would like to thank the many researchers, partners and supporters in this comprehensive monitoring effort. In particular, the Trust has worked closely with the National Oceanic and Atmospheric Administration (NOAA) to implement the monitoring program with significant funding through the American Recovery and Reinvestment Act and other NOAA programs. We would also like to acknowledge the involvement of the U.S. Fish & Wildlife Service, Maine Department of Marine Resources, Maine Department of Inland Fisheries and Wildlife, United States Geological Survey, Penobscot Indian Nation, The Nature Conservancy, The University of Maine, University of Southern Maine, Gulf of Maine Research Institute, Diadromous Species Restoration Research Network, Boyle Associates, Black Bear Hydro, LLC, and others that continue to make this work successful.

The Penobscot River Restoration Trust is the non-profit responsible for carrying out the restoration effort, including purchase of the Veazie, Great Works, and Howland dams in 2010. The Penobscot Trust removed the Great Works Dam in 2012, and will remove the Veazie Dam and decommission and build a bypass around the Howland Dam. Combined with additional fish passage enhancements at four other dams owned by Black Bear Hydro, the project will significantly improve access to nearly 1000 miles of habitat for sea-run fish. Energy enhancements at Black Bear Hydro facilities means energy production will remain at least the same as when the Project began, and likely increase. The Penobscot Trust board includes representatives from the Penobscot Indian Nation, American Rivers, Atlantic Salmon Federation, Maine Audubon, Natural Resources Council of Maine, Trout Unlimited, and The Nature Conservancy, along with three additional directors.